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The feasibility of variational quantum algorithms, the most popular correspondent of neural networks on noisy, near-term quantum hardware, is highly impacted by the circuit depth of the involved parametrized quantum circuits (PQCs). Higher depth increases expressivity, but also results in a detrimental accumulation of errors. Furthermore, the number of parameters involved in the PQC significantly influences the performance through the necessary number of measurements to evaluate gradients, which scales linearly with the number of parameters. Motivated by this, we look at deep equilibrium models (DEQs), which mimic an infinite-depth, weight-tied network using a fraction of the memory by employing a root solver to find the fixed points of the network. In this work, we present Quantum Deep Equilibrium Models (QDEQs): a training paradigm that learns parameters of a quantum machine learning model given by a PQC using DEQs. To our knowledge, no work has yet explored the application of DEQs to QML models. We apply QDEQs to find the parameters of a quantum circuit in two settings: the first involves classifying MNIST-4 digits with 4 qubits; the second extends it to 10 classes of MNIST, FashionMNIST and CIFAR. We find that QDEQ is not only competitive with comparable existing baseline models, but also achieves higher performance than a network with 5 times more layers. This demonstrates that the QDEQ paradigm can be used to develop significantly more shallow quantum circuits for a given task, something which is essential for the utility of near-term quantum computers. Our code is available at https://github.com/martaskrt/qdeq., Comment: To be published in NeurIPS 2024

Bayesian optimization (BO) has become an indispensable tool for autonomous decision-making across diverse applications from autonomous vehicle control to accelerated drug and materials discovery. With the growing interest in self-driving laboratories, BO of chemical systems is crucial for machine learning (ML) guided experimental planning. Typically, BO employs a regression surrogate model to predict the distribution of unseen parts of the search space. However, for the selection of molecules, picking the top candidates with respect to a distribution, the relative ordering of their properties may be more important than their exact values. In this paper, we introduce Rank-based Bayesian Optimization (RBO), which utilizes a ranking model as the surrogate. We present a comprehensive investigation of RBO's optimization performance compared to conventional BO on various chemical datasets. Our results demonstrate similar or improved optimization performance using ranking models, particularly for datasets with rough structure-property landscapes and activity cliffs. Furthermore, we observe a high correlation between the surrogate ranking ability and BO performance, and this ability is maintained even at early iterations of BO optimization when using ranking surrogate models. We conclude that RBO is an effective alternative to regression-based BO, especially for optimizing novel chemical compounds., Comment: 14 + 4 pages, 5 + 3 figures

Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's h-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's h-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks., Comment: Accepted as Spotlight at Conference on Neural Information Processing Systems (NeurIPS 2024)

In machine learning datasets with symmetries, the paradigm for backward compatibility with symmetry-breaking has been to relax equivariant architectural constraints, engineering extra weights to differentiate symmetries of interest. However, this process becomes increasingly over-engineered as models are geared towards specific symmetries/asymmetries hardwired of a particular set of equivariant basis functions. In this work, we introduce symmetry-cloning, a method for inducing equivariance in machine learning models. We show that general machine learning architectures (i.e., MLPs) can learn symmetries directly as a supervised learning task from group equivariant architectures and retain/break the learned symmetry for downstream tasks. This simple formulation enables machine learning models with group-agnostic architectures to capture the inductive bias of group-equivariant architectures.

Machine learning has been pervasively touching many fields of science. Chemistry and materials science are no exception. While machine learning has been making a great impact, it is still not reaching its full potential or maturity. In this perspective, we first outline current applications across a diversity of problems in chemistry. Then, we discuss how machine learning researchers view and approach problems in the field. Finally, we provide our considerations for maximizing impact when researching machine learning for chemistry.

Hamiltonian simulation using product formulas is arguably the most straightforward and practical approach for algorithmic simulation of a quantum system's dynamics on a quantum computer. Here we present corrected product formulas (CPFs), a variation of product formulas achieved by injecting auxiliary terms called correctors into standard product formulas. We establish several correctors that greatly improve the accuracy of standard product formulas for simulating Hamiltonians comprised of two partitions that can be exactly simulated, a common feature of lattice Hamiltonians, while only adding a small additive or multiplicative factor to the simulation cost. We show that correctors are particularly advantageous for perturbed systems, where one partition has a relatively small norm compared to the other, as they allow the small norm to be utilized as an additional parameter for controlling the simulation error. We demonstrate the performance of CPFs by numerical simulations for several lattice Hamiltonians. Numerical results show our theoretical error bound for CPFs matches or exceeds the empirical error of standard product formulas for these systems. CPFs could be a valuable algorithmic tool for early fault-tolerant quantum computers with limited computing resources. As for standard product formulas, CPFs could also be used for simulations on a classical computer., Comment: 30 pages; 3 figures (issue with references fixed)

Understanding is a crucial yet elusive concept in artificial intelligence (AI). This work proposes a framework for analyzing understanding based on the notion of composability. Given any subject (e.g., a person or an AI), we suggest characterizing its understanding of an object in terms of its ability to process (compose) relevant inputs into satisfactory outputs from the perspective of a verifier. This highly universal framework can readily apply to non-human subjects, such as AIs, non-human animals, and institutions. Further, we propose methods for analyzing the inputs that enhance output quality in compositions, which we call catalysts. We show how the structure of a subject can be revealed by analyzing its components that act as catalysts and argue that a subject's learning ability can be regarded as its ability to compose inputs into its inner catalysts. Finally we examine the importance of learning ability for AIs to attain general intelligence. Our analysis indicates that models capable of generating outputs that can function as their own catalysts, such as language models, establish a foundation for potentially overcoming existing limitations in AI understanding., Comment: 13 pages, 3 figures

Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at http://github.com/zoom-wang112358/MOLLEO

The industrial manufacturing of chemicals consumes a significant amount of energy and raw materials. In principle, the development of new catalysts could greatly improve the efficiency of chemical production. However, the discovery of viable catalysts can be exceedingly challenging because it is difficult to know the efficacy of a candidate without experimentally synthesizing and characterizing it. This study explores the feasibility of using fault-tolerant quantum computers to accelerate the discovery of homogeneous catalysts for nitrogen fixation, an industrially important chemical process. It introduces a set of ground-state energy estimation problems representative of calculations needed for the discovery of homogeneous catalysts and analyzes them on three dimensions: economic utility, classical hardness, and quantum resource requirements. For the highest utility problem considered, two steps of a catalytic cycle for the generation of cyanate anion from dinitrogen, the economic utility of running these computations is estimated to be $200,000, and the required runtime for double-factorized phase estimation on a fault-tolerant superconducting device is estimated under conservative assumptions to be 139,000 QPU-hours. The computational cost of an equivalent DMRG calculation is estimated to be about 400,000 CPU-hours. These results suggest that, with continued development, it will be feasible for fault-tolerant quantum computers to accelerate the discovery of homogeneous catalysts., Comment: 27 pages, 11 tables, 8 figures plus appendix

As applications of machine learning proliferate, innovative algorithms inspired by specific real-world challenges have become increasingly important. Such work offers the potential for significant impact not merely in domains of application but also in machine learning itself. In this paper, we describe the paradigm of application-driven research in machine learning, contrasting it with the more standard paradigm of methods-driven research. We illustrate the benefits of application-driven machine learning and how this approach can productively synergize with methods-driven work. Despite these benefits, we find that reviewing, hiring, and teaching practices in machine learning often hold back application-driven innovation. We outline how these processes may be improved., Comment: 12 pages, 3 figures

Visual recognition of materials and their states is essential for understanding the physical world, from identifying wet regions on surfaces or stains on fabrics to detecting infected areas on plants or minerals in rocks. Collecting data that captures this vast variability is complex due to the scattered and gradual nature of material states. Manually annotating real-world images is constrained by cost and precision, while synthetic data, although accurate and inexpensive, lacks real-world diversity. This work aims to bridge this gap by infusing patterns automatically extracted from real-world images into synthetic data. Hence, patterns collected from natural images are used to generate and map materials into synthetic scenes. This unsupervised approach captures the complexity of the real world while maintaining the precision and scalability of synthetic data. We also present the first comprehensive benchmark for zero-shot material state segmentation, utilizing real-world images across a diverse range of domains, including food, soils, construction, plants, liquids, and more, each appears in various states such as wet, dry, infected, cooked, burned, and many others. The annotation includes partial similarity between regions with similar but not identical materials and hard segmentation of only identical material states. This benchmark eluded top foundation models, exposing the limitations of existing data collection methods. Meanwhile, nets trained on the infused data performed significantly better on this and related tasks. The dataset, code, and trained model are available. We also share 300,000 extracted textures and SVBRDF/PBR materials to facilitate future datasets generation.

We present a generative diffusion model specifically tailored to the discovery of surface structures. The generative model takes into account substrate registry and periodicity by including masked atoms and $z$-directional confinement. Using a rotational equivariant neural network architecture, we design a method that trains a denoiser-network for diffusion alongside a force-field for guided sampling of low-energy surface phases. An effective data-augmentation scheme for training the denoiser-network is proposed to scale generation far beyond structure sizes represented in the training data. We showcase the generative model by investigating multiple surface systems and propose an atomistic structure model for a previously unknown silver-oxide domain-boundary of unprecedented size.

Generative machine learning methods such as large-language models are revolutionizing the creation of text and images. While these models are powerful they also harness a large amount of computational resources. The transformer is a key component in large language models that aims to generate a suitable completion of a given partial sequence. In this work, we investigate transformer architectures under the lens of fault-tolerant quantum computing. The input model is one where trained weight matrices are given as block encodings and we construct the query, key, and value matrices for the transformer. We show how to prepare a block encoding of the self-attention matrix, with a new subroutine for the row-wise application of the softmax function. In addition, we combine quantum subroutines to construct important building blocks in the transformer, the residual connection and layer normalization, and the feed-forward neural network. Our subroutines prepare an amplitude encoding of the transformer output, which can be measured to obtain a prediction. Based on common open-source large-language models, we provide insights into the behavior of important parameters determining the run time of the quantum algorithm. We discuss the potential and challenges for obtaining a quantum advantage., Comment: 31 pages, 4 figures, 2 tables, comments are welcome

The discovery of small molecules with therapeutic potential is a long-standing challenge in chemistry and biology. Researchers have increasingly leveraged novel computational techniques to streamline the drug development process to increase hit rates and reduce the costs associated with bringing a drug to market. To this end, we introduce a quantum-classical generative model that seamlessly integrates the computational power of quantum algorithms trained on a 16-qubit IBM quantum computer with the established reliability of classical methods for designing small molecules. Our hybrid generative model was applied to designing new KRAS inhibitors, a crucial target in cancer therapy. We synthesized 15 promising molecules during our investigation and subjected them to experimental testing to assess their ability to engage with the target. Notably, among these candidates, two molecules, ISM061-018-2 and ISM061-22, each featuring unique scaffolds, stood out by demonstrating effective engagement with KRAS. ISM061-018-2 was identified as a broad-spectrum KRAS inhibitor, exhibiting a binding affinity to KRAS-G12D at $1.4 \mu M$. Concurrently, ISM061-22 exhibited specific mutant selectivity, displaying heightened activity against KRAS G12R and Q61H mutants. To our knowledge, this work shows for the first time the use of a quantum-generative model to yield experimentally confirmed biological hits, showcasing the practical potential of quantum-assisted drug discovery to produce viable therapeutics. Moreover, our findings reveal that the efficacy of distribution learning correlates with the number of qubits utilized, underlining the scalability potential of quantum computing resources. Overall, we anticipate our results to be a stepping stone towards developing more advanced quantum generative models in drug discovery.

Automation is one of the cornerstones of contemporary material discovery. Bayesian optimization (BO) is an essential part of such workflows, enabling scientists to leverage prior domain knowledge into efficient exploration of a large molecular space. While such prior knowledge can take many forms, there has been significant fanfare around the ancillary scientific knowledge encapsulated in large language models (LLMs). However, existing work thus far has only explored LLMs for heuristic materials searches. Indeed, recent work obtains the uncertainty estimate -- an integral part of BO -- from point-estimated, non-Bayesian LLMs. In this work, we study the question of whether LLMs are actually useful to accelerate principled Bayesian optimization in the molecular space. We take a sober, dispassionate stance in answering this question. This is done by carefully (i) viewing LLMs as fixed feature extractors for standard but principled BO surrogate models and by (ii) leveraging parameter-efficient finetuning methods and Bayesian neural networks to obtain the posterior of the LLM surrogate. Our extensive experiments with real-world chemistry problems show that LLMs can be useful for BO over molecules, but only if they have been pretrained or finetuned with domain-specific data., Comment: ICML 2024. Code: https://github.com/wiseodd/lapeft-bayesopt

Simulating chemical systems is highly sought after and computationally challenging, as the simulation cost exponentially increases with the system size. Quantum computers have been proposed as a computational means to overcome this bottleneck. Most efforts recently have been spent on determining the ground states of chemical systems. Hardness results and the lack of efficient heuristics for initial-state generation sheds doubt on the feasibility. Here we propose an inherently efficient approach for solving chemical simulation problems, meaning it requires quantum circuits of size scaling polynomially in relevant system parameters. If a set of assumptions can be satisfied, our approach finds good initial states by assembling initial states for dynamical simulation in a scattering tree. We discuss a variety of quantities of chemical interest that can be measured based on quantum simulation, e.g. of a reaction, succeeding the initial state preparation., Comment: 12 pages, 4 figures

Advancements in large language models (LLMs) have demonstrated their potential in facilitating high-level reasoning, logical reasoning and robotics planning. Recently, LLMs have also been able to generate reward functions for low-level robot actions, effectively bridging the interface between high-level planning and low-level robot control. However, the challenge remains that even with syntactically correct plans, robots can still fail to achieve their intended goals due to imperfect plans or unexpected environmental issues. To overcome this, Vision Language Models (VLMs) have shown remarkable success in tasks such as visual question answering. Leveraging the capabilities of VLMs, we present a novel framework called Robotic Replanning with Perception and Language Models (RePLan) that enables online replanning capabilities for long-horizon tasks. This framework utilizes the physical grounding provided by a VLM's understanding of the world's state to adapt robot actions when the initial plan fails to achieve the desired goal. We developed a Reasoning and Control (RC) benchmark with eight long-horizon tasks to test our approach. We find that RePLan enables a robot to successfully adapt to unforeseen obstacles while accomplishing open-ended, long-horizon goals, where baseline models cannot, and can be readily applied to real robots. Find more information at https://replan-lm.github.io/replan.github.io/

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups., Comment: Accepted to Chemical Science Journal. Models are publicly available via https://huggingface.co/insilicomedicine/nach0_base and https://huggingface.co/insilicomedicine/nach0_large

Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann distribution, as determined by the molecule's energy. The proposed approach can be used in combination with energy estimation methods of different fidelity and discovers a diverse set of low-energy conformations for highly flexible drug-like molecules. We demonstrate that GFlowNet can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution.

Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Using these moments, Kraitchman analysis determines isotopic substitution coordinates, which are the unsigned $|x|,|y|,|z|$ coordinates of all atoms with natural isotopic abundance, including carbon, nitrogen, and oxygen. While unsigned substitution coordinates can verify guesses of structures, the missing $+/-$ signs make it challenging to determine the actual structure from the substitution coordinates alone. To tackle this inverse problem, we develop KREED (Kraitchman REflection-Equivariant Diffusion), a generative diffusion model that infers a molecule's complete 3D structure from its molecular formula, moments of inertia, and unsigned substitution coordinates of heavy atoms. KREED's top-1 predictions identify the correct 3D structure with >98% accuracy on the QM9 and GEOM datasets when provided with substitution coordinates of all heavy atoms with natural isotopic abundance. When substitution coordinates are restricted to only a subset of carbons, accuracy is retained at 91% on QM9 and 32% on GEOM. On a test set of experimentally measured substitution coordinates gathered from the literature, KREED predicts the correct all-atom 3D structure in 25 of 33 cases, demonstrating experimental applicability for context-free 3D structure determination with rotational spectroscopy., Comment: added software citations

Wavelet transforms are widely used in various fields of science and engineering as a mathematical tool with features that reveal information ignored by the Fourier transform. Unlike the Fourier transform, which is unique, a wavelet transform is specified by a sequence of numbers associated with the type of wavelet used and an order parameter specifying the length of the sequence. While the quantum Fourier transform, a quantum analog of the classical Fourier transform, has been pivotal in quantum computing, prior works on quantum wavelet transforms~(QWTs) were limited to the second and fourth order of a particular wavelet, the Daubechies wavelet. Here we develop a simple yet efficient quantum algorithm for executing any wavelet transform on a quantum computer. Our approach is to decompose the kernel matrix of a wavelet transform as a linear combination of unitaries (LCU) that are compilable by easy-to-implement modular quantum arithmetic operations and use the LCU technique to construct a probabilistic procedure to implement a QWT with a \textit{known} success probability. We then use properties of wavelets to make this approach deterministic by a few executions of the amplitude amplification strategy. We extend our approach to a multilevel wavelet transform and a generalized version, the packet wavelet transform, establishing computational complexities in terms of three parameters: the wavelet order $M$, the dimension $N$ of the transformation matrix, and the transformation level $d$. We show the cost is logarithmic in $N$, linear in $d$ and superlinear in $M$. Moreover, we show the cost is independent of $M$ for practical applications. Our proposed quantum wavelet transforms could be used in quantum computing algorithms in a similar manner to their well-established counterpart, the quantum Fourier transform., Comment: This version is identical in content to the published version. Presentation improved, typos fixed, and figures 1 and 2 added

Protein language models learn powerful representations directly from sequences of amino acids. However, they are constrained to generate proteins with only the set of amino acids represented in their vocabulary. In contrast, chemical language models learn atom-level representations of smaller molecules that include every atom, bond, and ring. In this work, we show that chemical language models can learn atom-level representations of proteins enabling protein generation unconstrained to the standard genetic code and far beyond it. In doing so, we show that language models can generate entire proteins atom by atom -- effectively learning the multiple hierarchical layers of molecular information that define proteins from their primary sequence to their secondary, and tertiary structure. We demonstrate language models are able to explore beyond protein space -- generating proteins with modified sidechains that form unnatural amino acids. Even further, we find that language models can explore chemical space and protein space simultaneously and generate novel examples of protein-drug conjugates. The results demonstrate the potential for biomolecular design at the atom level using language models.

Materials acceleration platforms (MAPs) combine automation and artificial intelligence to accelerate the discovery of molecules and materials. They have potential to play a role in addressing complex societal problems such as climate change. Solar chemicals and fuels generation via heterogeneous CO2 photo(thermal)catalysis is a relatively unexplored process that holds potential for contributing towards an environmentally and economically sustainable future, and therefore a very promising application for MAP science and engineering. Here, we present a brief overview of how design and innovation in heterogeneous CO2 photo(thermal)catalysis, from materials discovery to engineering and scale-up, could benefit from MAPs. We discuss relevant design and performance descriptors and the level of automation of state-of-the-art experimental techniques, and we review examples of artificial intelligence in data analysis. Based on these precedents, we finally propose a MAP outline for autonomous and accelerated discoveries in the emerging field of solar chemicals and fuels sourced from CO2 photo(thermal)catalysis.

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science.

Partial differential equations (PDEs) are ubiquitous in science and engineering. Prior quantum algorithms for solving the system of linear algebraic equations obtained from discretizing a PDE have a computational complexity that scales at least linearly with the condition number $\kappa$ of the matrices involved in the computation. For many practical applications, $\kappa$ scales polynomially with the size $N$ of the matrices, rendering a polynomial-in-$N$ complexity for these algorithms. Here we present a quantum algorithm with a complexity that is polylogarithmic in $N$ but is independent of $\kappa$ for a large class of PDEs. Our algorithm generates a quantum state that enables extracting features of the solution. Central to our methodology is using a wavelet basis as an auxiliary system of coordinates in which the condition number of associated matrices is independent of $N$ by a simple diagonal preconditioner. We present numerical simulations showing the effect of the wavelet preconditioner for several differential equations. Our work could provide a practical way to boost the performance of quantum-simulation algorithms where standard methods are used for discretization., Comment: 5 pages main text, 14 pages in total including appendix, 2 figures; updated references and fixed typos in this version

Language models are powerful tools for molecular design. Currently, the dominant paradigm is to parse molecular graphs into linear string representations that can easily be trained on. This approach has been very successful, however, it is limited to chemical structures that can be completely represented by a graph -- like organic molecules -- while materials and biomolecular structures like protein binding sites require a more complete representation that includes the relative positioning of their atoms in space. In this work, we show how language models, without any architecture modifications, trained using next-token prediction -- can generate novel and valid structures in three dimensions from various substantially different distributions of chemical structures. In particular, we demonstrate that language models trained directly on sequences derived directly from chemical file formats like XYZ files, Crystallographic Information files (CIFs), or Protein Data Bank files (PDBs) can directly generate molecules, crystals, and protein binding sites in three dimensions. Furthermore, despite being trained on chemical file sequences -- language models still achieve performance comparable to state-of-the-art models that use graph and graph-derived string representations, as well as other domain-specific 3D generative models. In doing so, we demonstrate that it is not necessary to use simplified molecular representations to train chemical language models -- that they are powerful generative models capable of directly exploring chemical space in three dimensions for very different structures.

Estimation of the expectation value of observables is a key subroutine in quantum computing and is also the bottleneck of the performance of many near-term quantum algorithms. Many works have been proposed to reduce the number of measurements needed for this task and they provide different measurement schemes for generating the measurements to perform. In this paper, we propose a new approach, composite measurement scheme, which composes multiple measurement schemes by distributing shots to them with a trainable ratio. As an example of our method, we study the case where only Pauli measurements are allowed and propose Composite-LBCS (C-LBCS), a composite measurement scheme made by composing locally-biased classical shadows. We numerically demonstrate C-LBCS on molecular systems up to $\mathrm{CO}_2$ (30 qubits) and show that C-LBCS outperforms the previous state-of-the-art methods despite its simplicity. We also show that C-LBCS can be efficiently optimized by stochastic gradient descent and is trainable even when the observable contains a large number of terms. We believe our method opens up a reliable way toward efficient observable estimation on large quantum systems., Comment: 12 pages, 2 figures

Generating low-level robot task plans from high-level natural language instructions remains a challenging problem. Although large language models have shown promising results in generating plans, the accuracy of the output remains unverified. Furthermore, the lack of domain-specific language data poses a limitation on the applicability of these models. In this paper, we propose CLAIRIFY, a novel approach that combines automatic iterative prompting with program verification to ensure programs written in data-scarce domain-specific language are syntactically valid and incorporate environment constraints. Our approach provides effective guidance to the language model on generating structured-like task plans by incorporating any errors as feedback, while the verifier ensures the syntactic accuracy of the generated plans. We demonstrate the effectiveness of CLAIRIFY in planning chemistry experiments by achieving state-of-the-art results. We also show that the generated plans can be executed on a real robot by integrating them with a task and motion planner.

Current quantum computing hardware is restricted by the availability of only few, noisy qubits which limits the investigation of larger, more complex molecules in quantum chemistry calculations on quantum computers in the near-term. In this work, we investigate the limits of their classical and near-classical treatment while staying within the framework of quantum circuits and the variational quantum eigensolver. To this end, we consider naive and physically motivated, classically efficient product ansatz for the parametrized wavefunction adapting the separable pair ansatz form. We combine it with post-treatment to account for interactions between subsystems originating from this ansatz. The classical treatment is given by another quantum circuit that has support between the enforced subsystems and is folded into the Hamiltonian. To avoid an exponential increase in the number of Hamiltonian terms, the entangling operations are constructed from purely Clifford or near-Clifford circuits. While Clifford circuits can be simulated efficiently classically, they are not universal. In order to account for missing expressibility, near-Clifford circuits with only few, selected non-Clifford gates are employed. The exact circuit structure to achieve this objective is molecule-dependent and is constructed using simulated annealing and genetic algorithms. We demonstrate our approach on a set of molecules of interest and investigate the extent of our methodology's reach. Empirical validation of our approach using numerical simulations shows a reduction of the qubit count of up to a 50\% at a similar accuracy as compared to the separable-pair ansatz., Comment: 12 pages, 9 figures plus 3 pages, 8 figures appendix

Hamiltonian simulation is known to be one of the fundamental building blocks of a variety of quantum algorithms such as its most immediate application, that of simulating many-body systems to extract their physical properties. In this work, we present qSWIFT, a high-order randomized algorithm for Hamiltonian simulation. In qSWIFT, the required number of gates for a given precision is independent of the number of terms in Hamiltonian, while the systematic error is exponentially reduced with regards to the order parameter. In this respect, our qSWIFT is a higher-order counterpart of the previously proposed quantum stochastic drift protocol (qDRIFT), in which the number of gates scales linearly with the inverse of the precision required. We construct the qSWIFT channel and establish a rigorous bound for the systematic error quantified by the diamond norm. qSWIFT provides an algorithm to estimate given physical quantities using a system with one ancilla qubit, which is as simple as other product-formula-based approaches such as regular Trotter-Suzuki decompositions and qDRIFT. Our numerical experiment reveals that the required number of gates in qSWIFT is significantly reduced compared to qDRIFT. Particularly, the advantage is significant for problems where high precision is required; for example, to achieve a systematic relative propagation error of $10^{-6}$, the required number of gates in third-order qSWIFT is 1000 times smaller than that of qDRIFT., Comment: 23 pages, 7 figures

Transparent object perception is a crucial skill for applications such as robot manipulation in household and laboratory settings. Existing methods utilize RGB-D or stereo inputs to handle a subset of perception tasks including depth and pose estimation. However, transparent object perception remains to be an open problem. In this paper, we forgo the unreliable depth map from RGB-D sensors and extend the stereo based method. Our proposed method, MVTrans, is an end-to-end multi-view architecture with multiple perception capabilities, including depth estimation, segmentation, and pose estimation. Additionally, we establish a novel procedural photo-realistic dataset generation pipeline and create a large-scale transparent object detection dataset, Syn-TODD, which is suitable for training networks with all three modalities, RGB-D, stereo and multi-view RGB. Project Site: https://ac-rad.github.io/MVTrans/, Comment: Accepted to ICRA 2023; 6 pages, 4 figures, 4 tables

String-based molecular representations play a crucial role in cheminformatics applications, and with the growing success of deep learning in chemistry, have been readily adopted into machine learning pipelines. However, traditional string-based representations such as SMILES are often prone to syntactic and semantic errors when produced by generative models. To address these problems, a novel representation, SELF-referencIng Embedded Strings (SELFIES), was proposed that is inherently 100% robust, alongside an accompanying open-source implementation. Since then, we have generalized SELFIES to support a wider range of molecules and semantic constraints and streamlined its underlying grammar. We have implemented this updated representation in subsequent versions of \selfieslib, where we have also made major advances with respect to design, efficiency, and supported features. Hence, we present the current status of \selfieslib (version 2.1.1) in this manuscript., Comment: 11 pages, 2 figures

Quantum computers promise to impact industrial applications, for which quantum chemical calculations are required, by virtue of their high accuracy. This perspective explores the challenges and opportunities of applying quantum computers to drug design, discusses where they could transform industrial research and elaborates on what is needed to reach this goal.

Chemists need to perform many laborious and time-consuming experiments in the lab to discover and understand the properties of new materials. To support and accelerate this process, we propose a robot framework for manipulation that autonomously performs chemistry experiments. Our framework receives high-level abstract descriptions of chemistry experiments, perceives the lab workspace, and autonomously plans multi-step actions and motions. The robot interacts with a wide range of lab equipment and executes the generated plans. A key component of our method is constrained task and motion planning using PDDLStream solvers. Preventing collisions and spillage is done by introducing a constrained motion planner. Our planning framework can conduct different experiments employing implemented actions and lab tools. We demonstrate the utility of our framework on pouring skills for various materials and two fundamental chemical experiments for materials synthesis: solubility and recrystallization., Comment: Equal author contribution from Naruki Yoshikawa, Andrew Zou Li, Kourosh Darvish, Yuchi Zhao and Haoping Xu

We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to chemical representations, however, is nontrivial, necessitating kernels defined over structured inputs such as graphs, strings and bit vectors. By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry. Motivated by scenarios frequently encountered in experimental chemistry, we showcase applications for GAUCHE in molecular discovery and chemical reaction optimisation. The codebase is made available at https://github.com/leojklarner/gauche

Deep learning models that leverage large datasets are often the state of the art for modelling molecular properties. When the datasets are smaller (< 2000 molecules), it is not clear that deep learning approaches are the right modelling tool. In this work we perform an extensive study of the calibration and generalizability of probabilistic machine learning models on small chemical datasets. Using different molecular representations and models, we analyse the quality of their predictions and uncertainties in a variety of tasks (binary, regression) and datasets. We also introduce two simulated experiments that evaluate their performance: (1) Bayesian optimization guided molecular design, (2) inference on out-of-distribution data via ablated cluster splits. We offer practical insights into model and feature choice for modelling small chemical datasets, a common scenario in new chemical experiments. We have packaged our analysis into the DIONYSUS repository, which is open sourced to aid in reproducibility and extension to new datasets., Comment: 15+4 pages, 9+3 figures Comments: Fix author name typo in article and meta data

Visual recognition of materials and their states is essential for understanding most aspects of the world, from determining whether food is cooked, metal is rusted, or a chemical reaction has occurred. However, current image recognition methods are limited to specific classes and properties and can't handle the vast number of material states in the world. To address this, we present MatSim: the first dataset and benchmark for computer vision-based recognition of similarities and transitions between materials and textures, focusing on identifying any material under any conditions using one or a few examples. The dataset contains synthetic and natural images. The synthetic images were rendered using giant collections of textures, objects, and environments generated by computer graphics artists. We use mixtures and gradual transitions between materials to allow the system to learn cases with smooth transitions between states (like gradually cooked food). We also render images with materials inside transparent containers to support beverage and chemistry lab use cases. We use this dataset to train a siamese net that identifies the same material in different objects, mixtures, and environments. The descriptor generated by this net can be used to identify the states of materials and their subclasses using a single image. We also present the first few-shot material recognition benchmark with images from a wide range of fields, including the state of foods and drinks, types of grounds, and many other use cases. We show that a net trained on the MatSim synthetic dataset outperforms state-of-the-art models like Clip on the benchmark and also achieves good results on other unsupervised material classification tasks., Comment: for associated code and dataset, see https://zenodo.org/record/7390166#.Y5ku6mHMJH4 or https://e1.pcloud.link/publink/show?code=kZIiSQZCYU5M4HOvnQykql9jxF4h0KiC5MX and https://icedrive.net/s/A13FWzZ8V2aP9T4ufGQ1N3fBZxDF

An efficient and expressive wavefunction ansatz is key to scalable solutions for complex many-body electronic structures. While Slater determinants are predominantly used for constructing antisymmetric electronic wavefunction ans\"{a}tze, this construction can result in limited expressiveness when the targeted wavefunction is highly complex. In this work, we introduce Waveflow, an innovative framework for learning many-body fermionic wavefunctions using boundary-conditioned normalizing flows. Instead of relying on Slater determinants, Waveflow imposes antisymmetry by defining the fundamental domain of the wavefunction and applying necessary boundary conditions. A key challenge in using normalizing flows for this purpose is addressing the topological mismatch between the prior and target distributions. We propose using O-spline priors and I-spline bijections to handle this mismatch, which allows for flexibility in the node number of the distribution while automatically maintaining its square-normalization property. We apply Waveflow to a one-dimensional many-electron system, where we variationally minimize the system's energy using variational quantum Monte Carlo (VQMC). Our experiments demonstrate that Waveflow can effectively resolve topological mismatches and faithfully learn the ground-state wavefunction., Comment: 12 pages, 7 figures

We introduce Group SELFIES, a molecular string representation that leverages group tokens to represent functional groups or entire substructures while maintaining chemical robustness guarantees. Molecular string representations, such as SMILES and SELFIES, serve as the basis for molecular generation and optimization in chemical language models, deep generative models, and evolutionary methods. While SMILES and SELFIES leverage atomic representations, Group SELFIES builds on top of the chemical robustness guarantees of SELFIES by enabling group tokens, thereby creating additional flexibility to the representation. Moreover, the group tokens in Group SELFIES can take advantage of inductive biases of molecular fragments that capture meaningful chemical motifs. The advantages of capturing chemical motifs and flexibility are demonstrated in our experiments, which show that Group SELFIES improves distribution learning of common molecular datasets. Further experiments also show that random sampling of Group SELFIES strings improves the quality of generated molecules compared to regular SELFIES strings. Our open-source implementation of Group SELFIES is available online, which we hope will aid future research in molecular generation and optimization., Comment: 11 pages + references and appendix

De novo drug design with desired biological activities is crucial for developing novel therapeutics for patients. The drug development process is time and resource-consuming, and it has a low probability of success. Recent advances in machine learning and deep learning technology have reduced the time and cost of the discovery process and therefore, improved pharmaceutical research and development. In this paper, we explore the combination of two rapidly-developing fields with lead candidate discovery in the drug development process. First, Artificial intelligence has already been demonstrated to successfully accelerate conventional drug design approaches. Second, quantum computing has demonstrated promising potential in different applications, such as quantum chemistry, combinatorial optimizations, and machine learning. This manuscript explores hybrid quantum-classical generative adversarial networks (GAN) for small molecule discovery. We substituted each element of GAN with a variational quantum circuit (VQC) and demonstrated the quantum advantages in the small drug discovery. Utilizing a VQC in the noise generator of a GAN to generate small molecules achieves better physicochemical properties and performance in the goal-directed benchmark than the classical counterpart. Moreover, we demonstrate the potential of a VQC with only tens of learnable parameters in the generator of GAN to generate small molecules. We also demonstrate the quantum advantage of a VQC in the discriminator of GAN. In this hybrid model, the number of learnable parameters is significantly less than the classical ones, and it can still generate valid molecules. The hybrid model with only tens of training parameters in the quantum discriminator outperforms the MLP-based one in terms of both generated molecule properties and the achieved KL divergence., Comment: 28 pages, 12 tables, 16 figures

Transitioning from fossil fuels to renewable energy sources is a critical global challenge; it demands advances at the levels of materials, devices, and systems for the efficient harvesting, storage, conversion, and management of renewable energy. Researchers globally have begun incorporating machine learning (ML) techniques with the aim of accelerating these advances. ML technologies leverage statistical trends in data to build models for prediction of material properties, generation of candidate structures, optimization of processes, among other uses; as a result, they can be incorporated into discovery and development pipelines to accelerate progress. Here we review recent advances in ML-driven energy research, outline current and future challenges, and describe what is required moving forward to best lever ML techniques. To start, we give an overview of key ML concepts. We then introduce a set of key performance indicators to help compare the benefits of different ML-accelerated workflows for energy research. We discuss and evaluate the latest advances in applying ML to the development of energy harvesting (photovoltaics), storage (batteries), conversion (electrocatalysis), and management (smart grids). Finally, we offer an outlook of potential research areas in the energy field that stand to further benefit from the application of ML.

In this work, we introduce a quantum-control-inspired method for the characterization of variational quantum circuits using the rank of the dynamical Lie algebra associated with the hermitian generator(s) of the individual layers. Layer-based architectures in variational algorithms for the calculation of ground-state energies of physical systems are taken as the focus of this exploration. A promising connection is found between the Lie rank, the accuracy of calculated energies, and the requisite depth to attain target states via a given circuit architecture, even when using a lot of parameters which is appreciably below the number of separate terms in the generators. As the cost of calculating the dynamical Lie rank via an iterative process grows exponentially with the number of qubits in the circuit and therefore becomes prohibitive quickly, reliable approximations thereto are desirable. The rapidity of the increase of the dynamical Lie rank in the first few iterations of the calculation is found to be a viable (lower bound) proxy for the full calculation, balancing accuracy and computational expense. We, therefore, propose the dynamical Lie rank and proxies thereof as a useful design metric for layer-structured quantum circuits in variational algorithms.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike., Comment: 29+21 pages, 6+19 figures, 6+2 tables

We introduce a family of variational quantum algorithms called quantum iterative power algorithms (QIPA) that outperform existing hybrid near-term quantum algorithms of the same kind. We demonstrate the capabilities of QIPA as applied to three different global-optimization numerical experiments: the ground-state optimization of the $H_2$ molecular dissociation, search of the transmon qubit ground-state, and biprime factorization. Since our algorithm is hybrid, quantum/classical technologies such as error mitigation and adaptive variational ansatzes can easily be incorporated into the algorithm. Due to the shallow quantum circuit requirements, we anticipate large-scale implementation and adoption of the proposed algorithm across current major quantum hardware., Comment: 17 pages, 7 figures

In this work, we introduce a new way to quantify information flow in quantum systems, especially for parameterized quantum circuits. We use a graph representation of the circuits and propose a new distance metric using the mutual information between gate nodes. We then present an optimization procedure for variational algorithms using paths based on the distance measure. We explore the features of the algorithm by means of the variational quantum eigensolver, in which we compute the ground state energies of the Heisenberg model. In addition, we employ the method to solve a binary classification problem using variational quantum classification. From numerical simulations, we show that our method can be successfully used for optimizing the parameterized quantum circuits primarily used in near-term algorithms. We further note that information-flow based paths can be used to improve convergence of existing stochastic gradient based methods.

As we continue to find applications where the currently available noisy devices exhibit an advantage over their classical counterparts, the efficient use of quantum resources is highly desirable. The notion of quantum autoencoders was proposed as a way for the compression of quantum information to reduce resource requirements. Here, we present a strategy to design quantum autoencoders using evolutionary algorithms for transforming quantum information into lower-dimensional representations. We successfully demonstrate the initial applications of the algorithm for compressing different families of quantum states. In particular, we point out that using a restricted gate set in the algorithm allows for efficient simulation of the generated circuits. This approach opens the possibility of using classical logic to find low representations of quantum data, using fewer computational resources.